Transcriptional pausing to scout ahead for DNA damage

Abstract

A cell’s genome is under constant threat of damage, which if not repaired can lead to mutations or cell death. Common forms of DNA damage found in nature include cyclobutane pyrimidine dimers and 6-4 photoproducts induced by UV-irradiation. These and other helix-distorting lesions are removed by a highly conserved process called nucleotide excision repair (NER) that is found in every kingdom of life (1). NER is initiated in two general ways: by damage recognition proteins that survey the entire genome for damage or lesion-induced transcriptional stalling. This latter pathway, called transcription-coupled repair (TCR), first reported in mammalian cells and then in bacteria, is initiated when RNA polymerase (RNAP) is arrested at a DNA lesion embedded in the transcribed strand (2, 3). However, before DNA repair enzymes obtain access, the stalled RNAP must be pushed away from the lesion by the action of DNA translocases. Thus, the repair “coupling factors,” which recognize the stalled RNAP, must work to both displace the polymerase and simultaneously enlist the repair proteins to remove the damage. In bacteria, two different TCR pathways have emerged involving two different DNA helicases, which help to displace RNAP. The Mfd (mutation frequency decline) protein, also called transcription-repair coupling factor, uses its helicase fold and ATP hydrolysis to literally push RNAP forward (downstream) past the damaged site (Fig. 1A) (reviewed in ref. 4), whereas in a newly discovered alternative pathway UvrD (helicase II) tows the RNAP backward (upstream) with the help of the transcription elongation factor, NusA (5). This second approach more closely resembles what is thought to occur in mammalian cells during TCR (6). As described below, Mfd targets the nucleotide excision repair system to sites of damage through its direct interaction with a stalled RNAP. However, nature has gone even further in devising ways to find and remove potentially RNAP-blocking DNA damage. As described by Haines et al. (7) in PNAS, Nigel Savery’s group at the University of Bristol have found that the Mfd protein that normally accompanies the translocating RNAP can be sent ahead of a blocked RNAP to scout for damage in the transcribed strand and facilitate the recruitment of the bacterial NER machinery.